Identification of organic micro-pollutants in surface water using MS-based infrared ion spectroscopy

Comprehensive monitoring of organic micro-pollutants (OMPs) in drinking water sources relies on non-target screening (NTS) using liquid-chromatography and high-resolution mass spectrometry (LC-HRMS). Identification of OMPs is typically based on accurate mass and tandem mass spectrometry (MS/MS) data by matching against entries in compound databases and MS/MS spectral libraries. MS/MS spectra are, however, not always diagnostic for the full molecular structure and, moreover, emerging OMPs or OMP transformation products may not be present in libraries. Here we demonstrate how infrared ion spectroscopy (IRIS), an emerging MS-based method for structural elucidation, can aid in the identification of OMPs. IRIS measures the IR spectrum of an m/z-isolated ion in a mass spectrometer, providing an orthogonal diagnostic for molecular identification. Here, we demonstrate the workflow for identification of OMPs in river water and show how quantum-chemically predicted IR spectra can be used to screen potential candidates and suggest structural assignments. A crucial step herein is to define a set of candidate structures, presumably including the actual OMP, for which we present several strategies based on domain knowledge, the IR spectrum and MS/MS spectrum.

Effects of high pressure and temperature conditions on the chemical fate of flowback water related chemicals

Environmental risk assessment is generally based on atmospheric conditions for the modelling of chemical fate after entering the environment. However, during hydraulic fracturing, chemicals may be released deep underground. This study therefore focuses on the effects of high pressure and high temperature conditions on chemicals in flowback water to determine whether current environmental fate models need to be adapted in the context of downhole activities. Crushed shale and flowback water were mixed and exposed to different temperature (25-100 °C) and pressure (1-450 bar) conditions to investigate the effects they have on chemical fate. Samples were analysed using LC-HRMS based non-target screening. The results show that both high temperature and pressure conditions can impact the chemical fate of hydraulic fracturing related chemicals by increasing or decreasing concentrations via processes of transformation, sorption, degradation and/or dissolution. Furthermore, the degree and direction of change is chemical specific. The change is lower or equal to a factor of five, but for a few individual compounds the degree of change can exceed this factor of five. This suggests that environmental fate models based on surface conditions may be used for an approximation of chemical fate under downhole conditions by applying an additional factor of five to account for these uncertainties. More accurate insight into chemical fate under downhole conditions may be gained by studying a fluid of known chemical composition and an increased variability in temperature and pressure conditions including concentration, salinity and pH as variables.

Comparing conventional and green fracturing fluids by chemical characterisation and effect-based screening

There is public and scientific concern about air, soil and water contamination and possible adverse environmental and human health effects as a result of hydraulic fracturing activities. The use of greener chemicals in fracturing fluid aims to mitigate these effects. This study compares fracturing fluids marketed as either 'conventional' or 'green', as assessed by their chemical composition and their toxicity in bioassays. Chemical composition was analysed via non-target screening using liquid chromatography - high resolution mass spectrometry, while toxicity was evaluated by the Ames fluctuation test to assess mutagenicity and CALUX reporter gene assays to determine specific toxicity. Overall, the results do not indicate that the 'green' fluids are less harmful than the 'conventional' ones. First, there is no clear indication that the selected green fluids contain chemicals present at lower concentrations than the selected conventional fluids. Second, the predicted environmental fate of the identified compounds does not seem to be clearly distinct between the 'green' and 'conventional' fluids, based on the available data for the top five chemicals based on signal intensity that were tentatively identified. Furthermore, Ames fluctuation test results indicate that the green fluids have a similar genotoxic potential than the conventional fluids. Results of the CALUX reporter gene assays add to the evidence that there is no clear difference between the green and conventional fluids. These results do not support the claim that currently available and tested green-labeled fracturing fluids are environmentally more friendly alternatives to conventional fracturing fluids.

Risk-based prioritization of suspects detected in riverine water using complementary chromatographic techniques

Surface waters are widely used as drinking water sources and hence their quality needs to be continuously monitored. However, current routine monitoring programs are not comprehensive as they generally cover only a limited number of known pollutants and emerging contaminants. This study presents a risk-based approach combining suspect and non-target screening (NTS) to help extend the coverage of current monitoring schemes. In particular, the coverage of NTS was widened by combining three complementary separations modes: Reverse phase (RP), Hydrophilic interaction liquid chromatography (HILIC) and Mixed-mode chromatography (MMC). Suspect lists used were compiled from databases of relevant substances of very high concern (e.g., SVHCs) and the concentration of detected suspects was evaluated based on ionization efficiency prediction. Results show that suspect candidates can be prioritized based on their potential risk (i.e., hazard and exposure) by combining ionization efficiency-based concentration estimation, in vitro toxicity data or, if not available, structural alerts and QSAR.based toxicity predictions. The acquired information shows that NTS analyses have the potential to complement target analyses, allowing to update and adapt current monitoring programs, ultimately leading to improved monitoring of drinking water sources.

Online Prioritization of Toxic Compounds in Water Samples through Intelligent HRMS Data Acquisition

LC-HRMS-based nontarget screening (NTS) has become the method of choice to monitor organic micropollutants (OMPs) in drinking water and its sources. OMPs are identified by matching experimental fragmentation (MS2) spectra with library or in silico-predicted spectra. This requires informative experimental spectra and prioritization to reduce feature numbers, currently performed post data acquisition. Here, we propose a different prioritization strategy to ensure high-quality MS2 spectra for OMPs that pose an environmental or human health risk. This online prioritization triggers MS2 events based on detection of suspect list entries or isotopic patterns in the full scan or an additional MS2 event based on fragment ion(s)/patterns detected in a first MS2 spectrum. Triggers were determined using cheminformatics; potentially toxic compounds were selected based on the presence of structural alerts, in silico-fragmented, and recurring fragments and mass shifts characteristic for a given structural alert identified. After MS acquisition parameter optimization, performance of the online prioritization was experimentally examined. Triggered methods led to increased percentages of MS2 spectra and additional MS2 spectra for compounds with a structural alert. Application to surface water samples resulted in additional MS2 spectra of potentially toxic compounds, facilitating more confident identification and emphasizing the method's potential to improve monitoring studies.

Quantifying Positional Isomers (QPI) by Top-Down Mass Spectrometry

Proteomics has exposed a plethora of posttranslational modifications, but demonstrating functional relevance requires new approaches. Top-down proteomics of intact proteins has the potential to fully characterize protein modifications in terms of amount, site(s), and the order in which they are deposited on the protein; information that so far has been elusive to extract by shotgun proteomics. Data acquisition and analysis of intact multimodified proteins have however been a major challenge, in particular for positional isomers that carry the same number of modifications at different sites. Solutions were previously proposed to extract this information from fragmentation spectra, but these have so far mainly been limited to peptides and have entailed a large degree of manual interpretation. Here, we apply high-resolution Orbitrap fusion top-down analyses in combination with bioinformatics approaches to attempt to characterize multiple modified proteins and quantify positional isomers. Automated covalent fragment ion type definition, detection of mass precision and accuracy, and extensive use of replicate spectra increase sequence coverage and drive down false fragment assignments from 10% to 1.5%. Such improved performance in fragment assignment is key to localize and quantify modifications from fragment spectra. The method is tested by investigating positional isomers of Ubiquitin mixed in known concentrations, which results in quantification of high ratios at very low standard errors of the mean (<5%), as well as with synthetic phosphorylated peptides. Application to multiphosphorylated Bora provides an estimation of the so far unknown stoichiometry of the known set of phosphosites and uncovers new sites from hyperphosphorylated Bora.

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ETD fragmentation reveals the presence of positional isomers.

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For proteins up to 40 kDa these positional isomers can accurately be quantified.

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For in-vitro phosphorylated BoraNT a wide array of positional isomers is revealed.

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Use of Fragment ion FDR levels improve the quality of extracted stoichiometries.

Organic micropollutant removal in full-scale rapid sand filters used for drinking water treatment in The Netherlands and Belgium

Biological treatment processes have the potential to remove organic micropollutants (OMPs) during water treatment. The OMP removal capacity of conventional drinking water treatment processes such as rapid sand filters (RSFs), however, has not been studied in detail. We investigated OMP removal and transformation product (TP) formation in seven full-scale RSFs all treating surface water, using high-resolution mass spectrometry based quantitative suspect and non-target screening (NTS). Additionally, we studied the microbial communities with 16S rRNA gene amplicon sequencing (NGS) in both influent and effluent waters as well as the filter medium, and integrated these data to comprehensively assess the processes that affect OMP removal. In the RSF influent, 9 to 30 of the 127 target OMPs were detected. The removal efficiencies ranged from 0 to 93%. A data-driven workflow was established to monitor TPs, based on the combination of NTS feature intensity profiles between influent and effluent samples and the prediction of biotic TPs. The workflow identified 10 TPs, including molecular structure. Microbial community composition analysis showed similar community composition in the influent and effluent of most RSFs, but different from the filter medium, implying that specific microorganisms proliferate in the RSFs. Some of these are able to perform typical processes in water treatment such as nitrification and iron oxidation. However, there was no clear relationship between OMP removal efficiency and microbial community composition. The innovative combination of quantitative analyses, NTS and NGS allowed to characterize real scale biological water treatments, emphasizing the potential of bio-stimulation applications in drinking water treatment.

Integration of target analyses, non-target screening and effect-based monitoring to assess OMP related water quality changes in drinking water treatment

The ever-increasing production and use of chemicals lead to the occurrence of organic micro-pollutants (OMPs) in drinking water sources, and consequently the need for their removal during drinking water treatment. Due to the sheer number of OMPs, monitoring using targeted chemical analyses alone is not sufficient to assess drinking water quality as well as changes thereof during treatment. High-resolution mass spectrometry (HRMS) based non-target screening (NTS) as well as effect-based monitoring using bioassays are promising monitoring tools for a more complete assessment of water quality and treatment performance. Here, we developed a strategy that integrates data from chemical target analyses, NTS and bioassays. We applied it to the assessment of OMP related water quality changes at three drinking water treatment pilot installations. These installations included advanced oxidation processes, ultrafiltration in combination with reverse osmosis, and granular activated carbon filtration. OMPs relevant for the drinking water sector were spiked into the water treated in these installations. Target analyses, NTS and bioassays were performed on samples from all three installations. The NTS data was screened for predicted and known transformation products of the spike-in compounds. In parallel, trend profiles of NTS features were evaluated using multivariate analysis methods. Through integration of the chemical data with the biological effect-based results potential toxicity was accounted for during prioritization. Together, the synergy of the three analytical methods allowed the monitoring of OMPs and transformation products, as well as the integrative biological effects of the mixture of chemicals. Through efficient analysis, visualization and interpretation of complex data, the developed strategy enabled to assess water quality and the impact of water treatment from multiple perspectives. Such information could not be obtained by any of the three methods alone. The developed strategy thereby provides drinking water companies with an integrative tool for comprehensive water quality assessment.

Prioritizing anthropogenic chemicals in drinking water and sources through combined use of mass spectrometry and ToxCast toxicity data

Advancements in high-resolution mass spectrometry based methods have enabled a shift from pure target analysis to target, suspect and non-target screening analyses to detect chemicals in water samples. The multitude of suspect chemicals thereby detected needs to be prioritized for further identification, prior to health risk assessment and potential inclusion into monitoring programs. Here, we compare prioritization of chemicals in Dutch water samples based on relative intensities only to prioritization including hazard information based on high-throughput in vitro toxicity data. Over 1000 suspects detected in sewage treatment plant effluent, surface water, groundwater and drinking water samples were ranked based on their relative intensities. Toxicity data availability and density in the ToxCast database were determined and visualized for these suspects, also in regard to water relevant mechanisms of toxicity. More than 500 suspects could be ranked using occurrence/hazard ratios based on more than 1000 different assay endpoints. The comparison showed that different prioritization strategies resulted in significantly different ranking, with only 2 suspects prioritized based on occurrence among the top 20 in the hazard ranking. We therefore propose a novel scheme that integrates both exposure and hazard data, and efficiently prioritizes which features need to be confidently identified first.

Potential of Environmental Enrichment to Prevent Transgenerational Effects of Paternal Trauma

Adverse experiences in early life are risk factors for the development of behavioral and physiological symptoms that can lead to psychiatric and cognitive disorders later in life. Some of these symptoms can be transmitted to the offspring, in some cases by non-genomic mechanisms involving germ cells. Using a mouse model of unpredictable maternal separation and maternal stress, we show that postnatal trauma alters coping behaviors in adverse conditions in exposed males when adult and in their adult male progeny. The behavioral changes are accompanied by increased glucocorticoid receptor (GR) expression and decreased DNA methylation of the GR promoter in the hippocampus. DNA methylation is also decreased in sperm cells of exposed males when adult. Transgenerational transmission of behavioral symptoms is prevented by paternal environmental enrichment, an effect associated with the reversal of alterations in GR gene expression and DNA methylation in the hippocampus of the male offspring. These findings highlight the influence of both negative and positive environmental factors on behavior across generations and the plasticity of the epigenome across life.

Deciphering the Interplay among Multisite Phosphorylation, Interaction Dynamics, and Conformational Transitions in a Tripartite Protein System

Multisite phosphorylation is a common pathway to regulate protein function, activity, and interaction pattern in vivo, but routine biochemical analysis is often insufficient to identify the number and order of individual phosphorylation reactions and their mechanistic impact on the protein behavior. Here, we integrate complementary mass spectrometry (MS)-based approaches to characterize a multisite phosphorylation-regulated protein system comprising Polo-like kinase 1 (Plk1) and its coactivators Aurora kinase A (Aur-A) and Bora, the interplay of which is essential for mitotic entry after DNA damage-induced cell cycle arrest. Native MS and cross-linking-MS revealed that Aur-A/Bora-mediated Plk1 activation is accompanied by the formation of Aur-A/Bora and Plk1/Bora heterodimers. We found that the Aur-A/Bora interaction is independent of the Bora phosphorylation state, whereas the Plk1/Bora interaction is dependent on extensive Bora multisite phosphorylation. Bottom-up and top-down proteomics analyses showed that Bora multisite phosphorylation proceeds via a well-ordered sequence of site-specific phosphorylation reactions, whereby we could reveal the involvement of up to 16 phosphorylated Bora residues. Ion mobility spectrometry-MS demonstrated that this multisite phosphorylation primes a substantial structural rearrangement of Bora, explaining the interdependence between extensive Bora multisite phosphorylation and Plk1/Bora complex formation. These results represent a first benchmark of our multipronged MS strategy, highlighting its potential to elucidate the mechanistic and structural implications of multisite protein phosphorylation.

Epigenetic marking of sperm by post-translational modification of histones and protamines

BACKGROUND

The concept that individual traits can be acquired and transmitted by the germline through epigenetic mechanisms has gained recognition in the past years. However, epigenetic marks in sperm have not been are not well identified.

RESULTS

Using a novel proteomic approach that combines peptide-based bottom-up and intact protein top-down tandem mass spectrometry, we report the identification of epigenetic marks on histones and protamines in adult mouse sperm. We identified a total of 26 post-translational modifications (PTMs) on specific residues of the core histones H2B, H3 and H4, and the linker histone H1, four of which had not been described previously in any tissue or cell line. We also detected 11 novel PTMs on the protamines PRM1 and PRM2 and observed that they are present in specific combinations on individual protamines.

CONCLUSIONS

Both histones and protamines carry multiple PTMs in the adult mouse sperm. On protamines, specific PTM combinations might form a 'protamine code' similar to the 'histone code'. These findings suggest a potential role for PTMs on sperm histones and protamines in epigenetic signatures underlying transgenerational inheritance.

Epigenetic modifications of the neuroproteome

In the central nervous system, epigenetic processes are involved in a multitude of brain functions ranging from the development and differentiation of the nervous system through to higher-order cognitive processes such as learning and memory. This review summarises the current state of the art for the proteomic analysis of the epigenetic regulation of gene expression, in particular the PTM of histones, in the brain and cellular model systems. It describes the MS technologies that have helped the identification and analysis of histones, histone variants and PTMs in the brain. Strategies for the isolation of histones that allow the qualitative analysis of PTMs and their combinatorial patterns are introduced, methods for the relative and absolute quantification of histone PTMs are described, and future challenges are discussed.

Identification of combinatorial patterns of post-translational modifications on individual histones in the mouse brain

Post-translational modifications (PTMs) of proteins are biochemical processes required for cellular functions and signalling that occur in every sub-cellular compartment. Multiple protein PTMs exist, and are established by specific enzymes that can act in basal conditions and upon cellular activity. In the nucleus, histone proteins are subjected to numerous PTMs that together form a histone code that contributes to regulate transcriptional activity and gene expression. Despite their importance however, histone PTMs have remained poorly characterised in most tissues, in particular the brain where they are thought to be required for complex functions such as learning and memory formation. Here, we report the comprehensive identification of histone PTMs, of their combinatorial patterns, and of the rules that govern these patterns in the adult mouse brain. Based on liquid chromatography, electron transfer, and collision-induced dissociation mass spectrometry, we generated a dataset containing a total of 10,646 peptides from H1, H2A, H2B, H3, H4, and variants in the adult brain. 1475 of these peptides carried one or more PTMs, including 141 unique sites and a total of 58 novel sites not described before. We observed that these PTMs are not only classical modifications such as serine/threonine (Ser/Thr) phosphorylation, lysine (Lys) acetylation, and Lys/arginine (Arg) methylation, but also include several atypical modifications such as Ser/Thr acetylation, and Lys butyrylation, crotonylation, and propionylation. Using synthetic peptides, we validated the presence of these atypical novel PTMs in the mouse brain. The application of data-mining algorithms further revealed that histone PTMs occur in specific combinations with different ratios. Overall, the present data newly identify a specific histone code in the mouse brain and reveal its level of complexity, suggesting its potential relevance for higher-order brain functions.

Alcohol-inducible gene expression in transgenic Populus

We tested the efficiency and optimized the conditions for controlled alcohol-inducible transgene expression in Populus using gus as a reporter gene. Specificity of induction, efficiency in different organs, effect of three chemical inducers, and induction methods were tested using up to 10 independent transgenic events generated in two different Populus genotypes. The optimal inducer concentration and the duration of induction period were determined in dose-response and in time-course experiments. Under in vitro conditions, beta-glucuronidase (GUS) induction was efficient both in the aerial parts and in the roots of regenerated plantlets. Among the chemical inducers tested, ethanol was the most effective activator with no apparent phytotoxicity when concentrations were at or below 2%. After 5 days of treatment, fluorometrically-determined the GUS activity could be detected when inducing with ethanol at concentrations as low as 0.5%. Prolonged induction by ethanol vapors significantly increased the GUS activity in leaves from both the tissue culture plants and greenhouse-grown plants.

Structure and expression of duplicate AGAMOUS orthologues in poplar

To investigate the homeotic systems underlying floral development in a dioecious tree, and to provide tools for the manipulation of floral development, we have isolated two Populus trichocarpa genes, PTAG1 and PTAG2, homologous to the Arabidopsis floral homeotic gene AGAMOUS (AG). PTAG1 and PTAG2 are located on separate linkage groups, but their non-coding regions are highly similar, consistent with a phylogenetically recent duplication. Intron/exon structure is conserved in relation to AG and the Antirrhinum AG orthologue, PLENA (PLE), and low-stringency Southern analysis demonstrated the absence of additional genes in the poplar genome with significant PTAG1/2 homology. PTAG1 and PTAG2 exhibit an AG-like floral expression pattern, and phylogenetic analysis of the AG subfamily strongly supports evolutionary orthology to C-class organ identity genes. The high degree of similarity shared by PTAG1 and PTAG2 in both sequence (89% amino acid identity) and expression indicates that they are unlikely to be functionally associated with specification of tree gender. Unexpectedly, PTAG transcripts were consistently detected in vegetative tissues.

A DEFICIENS homolog from the dioecious tree black cottonwood is expressed in female and male floral meristems of the two-whorled, unisexual flowers

We isolated PTD, a member of the DEFICIENS (DEF) family of MADS box transcription factors, from the dioecious tree, black cottonwood (Populus trichocarpa). In females, in situ hybridization experiments showed that PTD mRNA was first detectable in cells on the flanks of the inflorescence meristem, before differentiation of individual flowers was visually detectable. In males, the onset of PTD expression was delayed until after individual flower differentiation had begun and floral meristems were developing. Although PTD was initially expressed throughout the inner whorl meristem in female and male flowers, its spatial expression pattern became sex-specific as reproductive primordia began to form. PTD expression was maintained in stamen primordia, but excluded from carpel primordia, as well as vegetative tissues. Although PTD is phylogenetically most closely related to the largely uncharacterized TM6 subfamily of the DEF/APETELA3(AP3)/TM6 group, its spatio-temporal expression patterns are more similar to that of DEF and AP3 than to other members of the TM6 subfamily.

Diverse effects of overexpression of LEAFY and PTLF, a poplar (Populus) homolog of LEAFY/FLORICAULA, in transgenic poplar and Arabidopsis

PTLF, the Populus trichocarpa homolog of LEAFY (LFY) and FLORICAULA, was cloned to assess its function in a dioecious tree species. In situ hybridization studies showed that the gene was expressed most strongly in developing inflorescences. Expression was also seen in leaf primordia and very young leaves, most notably in apical vegetative buds near inflorescences, but also in seedlings. Although ectopic expression of the PTLF cDNA in Arabidopsis accelerated flowering, only one of the many tested transgenic lines of Populus flowered precociously. The majority of trees within a population of 3-year-old transgenic hybrid Populus lines with PTLF constitutively expressed showed few differences when compared to controls. However, phenotypic effects on growth rate and crown development, but not flowering, were seen in some trees with strong PTLF expression and became manifest only as the trees aged. Competence to respond to overexpression of LFY varied widely among Populus genotypes, giving consistent early flowering in only a single male P. tremula x P. tremuloides hybrid and causing gender change in another hybrid genotype. PTLF activity appears to be subject to regulation that does not affect heterologously expressed LFY, and is dependent upon tree maturation. Both genes provide tools for probing the mechanisms of delayed competence to flower in woody plants.

Site-directed mutagenesis of glycosylation sites in the transforming growth factor-beta 1 (TGF beta 1) and TGF beta 2 (414) precursors and of cysteine residues within mature TGF beta 1: effects on secretion and bioactivity

The transforming growth factor-beta 1 (TGF beta 1) and -beta 2 (414) precursors both contain three predicted sites of N-linked glycosylation within their pro regions. These are located at amino acid residues 72, 140, and 241 for the TGF beta 2 (414) precursor and at residues 82, 136, and 176 for the TGF beta 1 precursor; both proteins contain mannose-6-phosphate (M-6-P) residues. The major sites of M-6-P addition are at Asn (82) and Asn (136), the first two sites of glycosylation, for the TGF beta 1 precursor. We now show that the major site of M-6-P addition within the TGF beta 2 (414) precursor is at Asn241, the third glycosylation site. To determine the importance of N-linked glycosylation to the secretion of TGF beta 1 and -beta 2, site-directed mutagenesis was used to change the Asn residues to Ser residues; the resulting DNAs were transfected into COS cells, and their supernatants were assayed for TGF beta activity. Substitution of Asn (241) of the TGF beta 2 (414) precursor resulted in an 82% decrease in secreted TGF beta 2 bioactivity. Mutation at Asn72 resulted in a 44% decrease, while mutation at Asn140 was without effect. Elimination of all three glycosylation sites resulted in undetectable levels of TGF beta 2. These results were compared with similar mutations made in the cDNA encoding the TGF beta 1 precursor. Mutagenesis of the two M-6-P-containing sites (Asn82 and Asn136) resulted in an 83% decrease in secreted TGF beta 1; replacement of Asn82 and Asn136 with Ser individually resulted in 85% and 42% decreases in activity, respectively. Substitution of Asn176 with Ser was without effect, while substitution of all three sites of glycosylation resulted in undetectable levels of TGF beta 1 activity, similar to the results obtained with TGF beta 2. The nine Cys residues within the mature region of TGF beta 1 were mutated to serine, and their effects on TGF beta 1 secretion were evaluated. Mutation of most Cys residues resulted in undetectable levels of TGF beta 1 protein or activity in conditioned medium. Mutation of Cys (355) led to the secretion of inactive TGF beta 1 monomers, suggesting that this residue is either directly involved in dimer formation or required for correct interchain disulfide bond formation.

Site-directed mutagenesis of cysteine residues in the pro region of the transforming growth factor beta 1 precursor. Expression and characterization of mutant proteins

Three cysteine residues are located in the pro region of the transforming growth factor beta 1 (TGF-beta 1) precursor at amino acid positions 33, 223, and 225. Previous studies (Gentry, L. E., Lioubin, M. N., Purchio, A. F., and Marquardt, H. (1988) Mol. Cell. Biol. 8, 4162-4168) with purified recombinant TGF-beta 1 (rTGF-beta 1) precursor produced by Chinese hamster ovary (CHO) cells revealed that Cys-33 can form a disulfide bond with at least 1 cysteine residue in mature TGF-beta 1, contributing to the formation of a 90-110-kDa protein. We now show that Cys-223 and Cys-225 form interchain disulfide bonds. Site-directed mutagenesis was used to change these Cys codons to Ser codons, and mutant constructs were transfected into COS cells. Analysis of recombinant proteins by immunoblotting showed that by substituting Cys-33 the 90-110-kDa protein is not formed, and thus, more mature dimer (24 kDa) is obtained, corresponding to a 3- to 5-fold increase in biological activity. Substitution of Cys-223 and/or Cys-225 resulted in near wild-type levels of mature TGF-beta 1. Furthermore, cells transfected with plasmid coding for Ser at positions 223 and 225 expressed only monomeric precursor proteins and released bioactive TGF-beta 1 that did not require acid activation, suggesting that dimerization of the precursor pro region may be necessary for latency.

Transforming growth factor beta 1: importance of glycosylation and acidic proteases for processing and secretion

The role of glycosylation of the transforming growth factor-beta 1 (TGF-beta 1) precursor was investigated by treating a transfected Chinese hamster ovary (CHO) cell line expressing high levels of recombinant TGF-beta 1 (TGF-beta 3-2000 cells) with a series of glycosylational inhibitors. Tunicamycin, a nucleoside antibiotic which prevents the formation of the dolichol intermediate necessary for oligosaccharide addition of the nascent polypeptide chain, appeared to block secretory exit and led to an increase in the cellular associated, nonglycosylated pro-TGF-beta 1 form. 1-Deoxymannojirimycin and swainsonine, inhibitors of the mannosidases I and II, respectively, blocked complete glycoprotein processing of the TGF-beta 1 precursor as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and by sensitivity to glycosidases. However, the abnormal TGF-beta 1 polypeptides containing the altered carbohydrate side chains were secreted readily by the CHO cells. In contrast, inhibitors of the glucosidases at the first step in glycoprotein remodeling, 1-deoxynojirimycin and castanospermine, markedly inhibited secretion of the TGF-beta 1 polypeptides from transfected CHO cells. In all cases, these inhibitors did not appear to affect proteolytic processing of the TGF-beta 1 polypeptides. Furthermore, inhibitor treatment did not affect mannose-6-phosphorylation of the TGF-beta 1 polypeptides. These results suggest that glycosylation and early stage remodeling of oligosaccharide side chains are necessary for secretion of TGF-beta 1. Treatment of the transfected CHO cells with weak bases (NH4Cl and chloroquine), or a monovalent ionophore (monensin), prevented proteolytic processing of the TGF-beta 1 precursor indicating that cleavage occurs by proteases in an acidic cellular compartment.

Identification of mannose 6-phosphate in two asparagine-linked sugar chains of recombinant transforming growth factor-beta 1 precursor

Recombinant transforming growth factor-beta 1 (TGF-beta 1) precursor produced and secreted by a clone of Chinese hamster ovary cells was found to be glycosylated and phosphorylated. Treatment of 32P-labeled precursor protein with N-glycanase indicated that phosphate was incorporated into asparagine-linked complex carbohydrate moieties. Fractionation of 32P-labeled glycopeptides followed by amino acid sequence analysis indicated that greater than 95% of the label was incorporated into two out of three glycosylation sites at Asn-82 and Asn-136 of the TGF-beta 1 precursor. Two-dimensional electrophoretic analysis of acid hydrolyzed precursor protein and precursor protein-derived glycopeptides indicated that 32P was incorporated as mannose 6-phosphate. Binding studies with the purified receptor for mannose 6-phosphate indicated that the TGF-beta 1 precursor could bind to this receptor and the binding was specifically inhibited with mannose 6-phosphate.

Recombinant type 1 transforming growth factor beta precursor produced in Chinese hamster ovary cells is glycosylated and phosphorylated

Analyses of cDNA clones coding for simian type 1 transforming growth factor beta (TGF-beta 1) suggest that there are three potential sites for N-linked glycosylation located in the amino terminus of the precursor region. Analysis of [3H]glucosamine-labeled serum-free supernatants from a line of Chinese hamster ovary cells which secrete high levels of recombinant TGF-beta 1 indicate that the TGF-beta 1 precursor, but not the mature form, is glycosylated. Digestion with neuraminidase resulted in a shift in migration of the two TGF-beta 1 precursor bands, which suggests that they contain sialic acid residues. Endoglycosidase H had no noticeable effect. Treatment with N-glycanase produced two faster-migrating sharp bands, the largest of which had a molecular weight of 39 kilodaltons. TGF-beta 1-specific transcripts produced by SP6 polymerase programmed the synthesis of a 42-kilodalton polypeptide which, we suggest, is the unmodified protein backbone of the precursor. Labeling with 32Pi showed that the TGF-beta 1 precursor was phosphorylated in the amino portion of the molecule.

Type 1 transforming growth factor beta: amplified expression and secretion of mature and precursor polypeptides in Chinese hamster ovary cells

Recombinant type 1 transforming growth factor beta (TGF-beta) was expressed to high levels in CHO cells by using dihydrofolate reductase (dhfr) gene amplification. The expression plasmid was derived from the pSV2 vectors and contained, in tandem, the simian TGF-beta and mouse dhfr cDNAs. Transcription of both cDNAs was controlled by the simian virus 40 early promoter. Stepwise selection of transfected CHO cells in increasing concentrations of methotrexate yielded cell lines that expressed amplified TGF-beta nucleic acid sequences. The expression plasmid DNA was amplified greater than 35-fold in one of the methotrexate-selected transfectants. The major proteins secreted by these cells consisted of latent TGF-beta and TGF-beta precursor polypeptides, as judged by immunoblots by using site-specific anti-peptide antibodies derived from various regions of the TGF-beta precursor. Levels of recombinant TGF-beta protein secreted by these cells approached 30 micrograms/24 h per 10(7) cells and required prior acidification for optimal activity; nonacidified supernatants were approximately 1% as active as acidified material. Antibodies directed toward sequences present in the mature growth factor readily identified a proteolytically processed recombinant TGF-beta which, on sodium dodecyl sulfate-polyacrylamide gels, comigrated with highly purified natural TGF-beta. In addition to mature recombinant TGF-beta, site-specific antibodies demonstrated the existence of larger TGF-beta precursor polypeptides. The availability of biologically active recombinant type 1 TGF-beta and precursor forms should provide a means to examine the structure, function, and potential in vivo therapeutic use of this growth factor.

Dual evolutionary modes in the bovine globin locus

Five bovine globin pseudogenes were subjected to sequence analysis. These genes include the three pseudogenes in the beta-type globin gene cluster as well as two allelic forms. Comparison of the sequences with those of the adult and fetal bovine globin genes shows that together they form a multigene family that was created by large-scale duplication. The structures are explained by invoking sequence exchange mediated by gene conversion. After their creation these genes evolved in a concerted fashion, exchanging sequence freely by intrachromosomal gene conversion. Subsequently, one by one, the genes were uncoupled from this exchange. This was accomplished by the creation of nonhomologies that formed barriers to gene conversion. These nonhomologies were several hundred bases in length and were formed by either deletion or by insertion of short repetitive sequences within the gene structures. In this way the genes made the transition from a rapid, coupled mode to a slow, solitary mode of evolution. Allelic gene polymorphisms were distributed inhomogeneously in the bovine globin family. It is proposed that this was due to interruption of interchromosomal gene conversion by a recent pseudogene duplication in the fetal globin gene cluster.